I see learning as very dependency based. Ie. there are a bunch of concepts you have to know. Think of them as nodes. These nodes have dependencies. As in you have to know A, B and C before you can learn D.

Spot on. This is a big problem is mathematics education; prior to university a lot of teaching is done without paying heed to the fundamental concepts. For example - here in the UK - calculus is taught well before limits (in fact limits aren't taught until students get to university).

Teaching is all about crossing the inferential distance between the student's current knowledge and the idea being taught. It's my impression that most people who say "you just have to practice," say as such because they don't know how to cross that gap. You see this often with professors who don't know how to teach their own subjects because they've forgotten what it was like not knowing how to calculate the expectation of a perturbed Hamiltonian. I suspect that in some cases the knowledge isn't truly a part of them, so that they don't know how to generate it without already knowing it.

Projects are a good way to help students retain information (the testing effect) and also train appropriate recall. Experts in a field are usually experts because they can look at a problem and see where they should be applying their knowledge - a skill that can only be effectively trained by 'real world' problems. In my experience teaching A-level math students, the best students are usually the ones that can apply concepts they've learned in non-obvious situations.

You might find this article I wrote on studying interesting.